First off, some options within FNEI were changed:
Unlocking the admin controls within FNEI (all three) and setting FNEI window to stay open (don't auto-close).

Then the game was played normally for the most part. at some point during play, i open FNEI to check a recipe or see what technology i need to research in order to get to a certain point.

Omnimatter isn't like most mods, it's very dynamic. it unlocks and locks recipes, overwrites its own recipes once research is completed, etc.

On this particular occassion, after checking a piece of research and opening the technology window, my omnitractor recipes disappeared. saving/reloading the game didn't restore them. opening FNEI and the technology window showed i had researched the necessary technology and normally (creative Mode+lots of OP beacons+reduced science cost) play through without using FNEI doing pretty much all the same things results with no losses in recipes within omnitractor.

Created a new world. activated most of the creativeMode cheats, and built a simple research factory that would research things quickly.
I took screenshots every so often but a few hours into the game i was well past my original "error" point and had many more omnitractor recipes available to me.
I opened FNEI, set the admin controls to let me use it to look into the technology window, clicked a technology icon for something and BOOM, all my recipes are missing for omnitractor.

https://www.dropbox.com/s/7xshj8917fb34io/FNEI%20deleted%20omnitractor%20recipes.rar?dl=0

zip file has screenshots, save files, and factorio-current.log

I forgot to include modsettings.dat, but i can send that too if you need it.

and specifically, the recipes that cause the behaviour are ones related to (used in) the omnitractor

my very-uneducated guess is that, somehow, the way omni handles disabling/enabling higher tier recipes in some function within his mod (when research is done) is getting called whenever FNEI tries to parse through/scan/traverse the technology tree. the function FNEI uses is triggering a recipe reset (or a technology-effect reset) somehow/somewhere.

i can create a more slimmed down save file with fewer mods if that helps, and more screencaps

a MUCH trimmed down playthrough with far fewer mods, and more screenshots for the first 5 minutes of play till i was able to cause the error.

https://www.dropbox.com/sh/vhlt045c1w97vfc/AAA56xrjZF-ZUx6BXCDgs8yPa?dl=0

As soon as Rubyte Ore extraction 3's technology icon is clicked (look through the screenshots), recipes for oil sand get deleted from omnitractor.

Somehow, the fNEI-method being used to scan the technology tree is triggering the function that omnimatter uses to dynamically enable/disable recipes based on what research is completed. My guess is that, once the technology tree (list of pre-requisites) is printed/returned to FNEI, and printed to screen, omnimatter is like "hey, this recipe for oil-sands (or whatever WASNT in the list of pre-requisites for the clicked-icon technology within FNEI----) ...shouldn't be enabled. okay, lets disable it"

Thank you for your detailed feedback. Now I do not have much time, so I'll study your problem in more detail later. I have already written more than once that the factorio does not support the possibility to open a technological tree for the technology we need, so we have to use a workaround that can cause such problems with non-standard modes. That's why it's possible to watch the technology tree through the mod only for admins and with their permission.

if it helps, i've used FNEI extensively in the past, in almost every world i've ever had, and always enable the admin options. and i don't recall this behaviour ever occurring before. and i believe that is due to the very-dynamic way omnimatter unlocks/update/overwrites/disables technology throughout a playthrough. Its mostly a hunch, and one i don't know how to test and verify the cause or formulate a solution--the best i got is a GUESS as to why this occurs specifically with omnimatter is tied to the work-around omni uses to update recipes...and whatever that method IS---is somehow getting called, and during the function call, it is passed incomplete technology-completion info due to only part of the technology tree getting printed/scanned by FNEI to whatever research is clicked on within your GUI----and somehow, the result is that recipes are removed from the omnitractor

located what i think is the triggering function within omnimatter that dynamically disabled recipes within control.lua of omnilib

line50 of control.lua "omnilib_2.0.11.zip": function omni_update(game)